NDLI: Long-read sequencing uncovers a complex transcriptome topology in varicella zoster virus

Content Provider	Springer Nature : BioMed Central
Author	Prazsák, István Moldován, Norbert Balázs, Zsolt Tombácz, Dóra Megyeri, Klára Szűcs, Attila Csabai, Zsolt Boldogkői, Zsolt
Abstract	Background Varicella zoster virus (VZV) is a human pathogenic alphaherpesvirus harboring a relatively large DNA molecule. The VZV transcriptome has already been analyzed by microarray and short-read sequencing analyses. However, both approaches have substantial limitations when used for structural characterization of transcript isoforms, even if supplemented with primer extension or other techniques. Among others, they are inefficient in distinguishing between embedded RNA molecules, transcript isoforms, including splice and length variants, as well as between alternative polycistronic transcripts. It has been demonstrated in several studies that long-read sequencing is able to circumvent these problems. Results In this work, we report the analysis of the VZV lytic transcriptome using the Oxford Nanopore Technologies sequencing platform. These investigations have led to the identification of 114 novel transcripts, including mRNAs, non-coding RNAs, polycistronic RNAs and complex transcripts, as well as 10 novel spliced transcripts and 25 novel transcription start site isoforms and transcription end site isoforms. A novel class of transcripts, the nroRNAs are described in this study. These transcripts are encoded by the genomic region located in close vicinity to the viral replication origin. We also show that the ORF63 exhibits a complex structural variation encompassing the splice sites of VZV latency transcripts. Additionally, we have detected RNA editing in a novel non-coding RNA molecule. Conclusions Our investigations disclosed a composite transcriptomic architecture of VZV, including the discovery of novel RNA molecules and transcript isoforms, as well as a complex meshwork of transcriptional read-throughs and overlaps. The results represent a substantial advance in the annotation of the VZV transcriptome and in understanding the molecular biology of the herpesviruses in general.
Related Links	https://bmcgenomics.biomedcentral.com/counter/pdf/10.1186/s12864-018-5267-8.pdf
Ending Page	20
Page Count	20
Starting Page	1
File Format	HTM / HTML
ISSN	14712164
DOI	10.1186/s12864-018-5267-8
Journal	BMC Genomics
Issue Number	1
Volume Number	19
Language	English
Publisher	BioMed Central
Publisher Date	2018-12-04
Access Restriction	Open
Subject Keyword	Life Sciences Microarrays Proteomics Animal Genetics and Genomics Microbial Genetics and Genomics Plant Genetics and Genomics Herpesvirus Varicella zoster virus Transcriptome Oxford Nanopore Technologies Long-read sequencing RNA editing nroRNA
Content Type	Text
Resource Type	Article
Subject	Biotechnology Genetics
Journal Impact Factor	3.5/2023
5-Year Journal Impact Factor	4.1/2023

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

Lytic Transcriptome Dataset of Varicella Zoster Virus Generated by Long-Read Sequencing

Long-read Sequencing Uncovers a Complex Transcriptome Topology in Varicella Zoster Virus

Profiling the polyadenylated transcriptome of extracellular vesicles with long-read nanopore sequencing

Illuminating the dark side of the human transcriptome with long read transcript sequencing

Assembling highly repetitive Xanthomonas TALomes using Oxford Nanopore sequencing

Consistent ultra-long DNA sequencing with automated slow pipetting

Kastor: a reference-based comparative approach for assessment and correction of gene-fragmenting errors in long-read assemblies of small genomes

Re-examination of two diatom reference genomes using long-read sequencing

Full-length isoform concatenation sequencing to resolve cancer transcriptome complexity

Long-read sequencing uncovers a complex transcriptome topology in varicella zoster virus

Similar Documents

Lytic Transcriptome Dataset of Varicella Zoster Virus Generated by Long-Read Sequencing

Long-read Sequencing Uncovers a Complex Transcriptome Topology in Varicella Zoster Virus

Profiling the polyadenylated transcriptome of extracellular vesicles with long-read nanopore sequencing

Illuminating the dark side of the human transcriptome with long read transcript sequencing

Assembling highly repetitive Xanthomonas TALomes using Oxford Nanopore sequencing

Consistent ultra-long DNA sequencing with automated slow pipetting

Kastor: a reference-based comparative approach for assessment and correction of gene-fragmenting errors in long-read assemblies of small genomes

Re-examination of two diatom reference genomes using long-read sequencing

Full-length isoform concatenation sequencing to resolve cancer transcriptome complexity

Long-read sequencing uncovers a complex transcriptome topology in varicella zoster virus